Investigation of melanoma treatments in mice and humans

Group - 24

Introduction

Dataset and general idea - What we wanted to do and why we chose that dataset - What did we intend to analyse in the datasets - What was our general goal for the project

Methods

Cleaning

  • How we cleaned the data and why

Augmentation

  • How we processed or data to prepare it for analysis
  • Why we did 0 handling and how
  • Why we did log2 fold expressions

Description (1)

  • Many zero expressions through cell lines in each of treatment

Description (2)

Results

Mouse gene expression analysis

  • Only 346 significantly regulated genes out of 39075
  • 0 handling making estimated treatment impact on expressions unsure.

Analysis of regulated Mouse genes across the 3 treatments

  • Approximately equal amounts of significantly regulated genes in each treatment

  • However, the overlap is very small

The human Analysis

  • PCA analysis across 18 human cell lines

  • PCA limitations underscore the complexity of gene regulation and its impact on cell line behavior

Discussion

  • Combined investigation across mouse and human melanoma cell lines provided valuable insights into the influences of the studied compounds and treatment effects on their gene expression patterns

  • Future work is needed to better understand the impact of these treatments on gene expression and cellular pathways across different melanoma cells ( selection of other promising cell candidates and compounds)

References

Jo Waaler (2022) Human melanoma cell lines treated with G007-LK. BioStudies, E-MTAB-8438. Retrieved from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-8438
Jo Waaler (2021). Mouse melanoma cell line B16-F10 treated with G007-LK. BioStudies, E-MTAB-8101. Retrieved from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-8101
Waaler, Jo, et al. “Tankyrase Inhibition Sensitizes Melanoma to PD-1 Immune Checkpoint Blockade in Syngeneic Mouse Models.” Communications Biology, vol. 3, no. 1, 24 Apr. 2020, https://doi.org/10.1038%2Fs42003-020-0916-2 Accessed 25 Nov. 2023
Martín‐Fernández, Josep Antoni, Javier Palarea‐Albaladejo, and Ricardo Antonio Olea. “Dealing with zeros.” Compositional data analysis: Theory and applications (2011): 43-58.